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Sample GSM989763 Query DataSets for GSM989763
Status Public on Aug 23, 2012
Title PC 237N
Sample type RNA
 
Channel 1
Source name reference RNA
Organism Homo sapiens
Characteristics reference: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PC 237N2
Organism Homo sapiens
Characteristics individual: PC 237N
disease state: Normal
tissue: prostate
Growth protocol All prostate samples used for this study were collected at the Stanford University Medical Center between 1999 and 2007 with patient's informed consent under an Institutional Review Board (IRB)-approved protocol. Multiple tissue samples were harvested from each prostate, flash-frozen and stored at 80oC. Frozen sections of each prostate sample were performed and evaluated by a genitourinary pathologist (JKM). The tumor and nontumor areas were marked and contaminating tissues were trimmed away from the block as described previously.48 Tumor samples in which at least 90% of the epithelial cells were cancerous were selected for extraction of DNA and RNA. In total, we selected 98 tumors from 86 patients that met these criteria. Associated clinical data were collected and included preoperative PSA levels, clinical stage, pathological stage, tumor Gleason grade and clinical follow-up. Recurrence was defined as a measurable serum PSA (>0.1ng/ml on two consecutive measurements) after surgery.
Gene-expression profiling was performed as reported. Briefly, Cy5-labeled cDNA was prepared by using 50ug of total RNA from prostate samples and Cy3-labeled cDNA was prepared by using common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines. For each experimental sample, Cy5- and Cy3-labeled samples were cohybridized to HEEBO spotted microarrays.49 HEEBO microarrays were manufactured in the Stanford Functional Genomics Facility at Stanford University and contained 44-544 70-mer probes.
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol After hybridization, microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments-Molecular Devices, LLC, Sunnyvale, CA, USA). Fluorescence ratios for array elements were extracted using GENEPIX software and uploaded into the Stanford Microarray Database for subsequent analysis.
Description Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81109.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 21, 2012
Last update date Aug 23, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL15973
Series (1)
GSE40272 Gene-expression profiling of prostate tumors

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 4327 3219 76 393 4251 2826 4936 3383 86 464 4859 2990 0 0 2840 1173 41 312 100 100 98 96 7077 7849 1.504 .665 .615 .956 .632 8.269 52 331 .528 .9 80 1770 6890 29 37 37 45 0 2852 348 2503 .589 2997 2649 1.698 .545 -.764 -.875
2 6174 3853 84 408 6090 3445 7407 4129 94 443 7323 3721 0 0 2781 1243 45 274 100 100 100 100 9535 11044 1.768 .566 .508 .616 .599 5.113 32 232 .51 .94 70 1930 6880 28 35 53 60 0 3413 361 3052 .501 3658 3296 1.996 .45 -.997 -1.152
3 3757 4460 85 372 3671 4088 4426 4639 94 428 4341 4267 0 0 1665 1325 47 293 100 100 100 100 7759 8608 .898 1.114 .983 1.368 1.065 7.852 32 232 1.002 .92 70 2070 6880 28 35 67 74 0 3951 330 3621 .986 4109 3780 1.014 .871 -.02 -.2
4 9181 4883 84 421 9097 4462 9351 4953 90 496 9267 4532 0 0 1453 966 46 366 100 100 100 100 13559 13799 2.039 .49 .489 .486 .488 4.357 32 216 .473 .93 70 2230 6890 29 36 83 90 0 4326 373 3953 .434 4388 4015 2.302 .433 -1.203 -1.207
5 391 253 62 270 329 -16 396 189 65 376 333 -80 0 0 52 159 28 419 100 0 100 0 313 253 null null null .415 .363 5.506 12 104 -.254 -.2 50 2370 6880 29 34 98 103 0 224 239 -14 null 167 -71 null null null null
6 1546 2170 82 342 1463 1827 1716 2172 90 419 1634 1829 0 0 626 917 43 295 100 98 100 90 3290 3463 .801 1.249 1.119 1.226 1.296 6.588 52 258 1.165 .86 80 2530 6880 28 36 113 121 0 1922 303 1618 1.106 1924 1620 .904 .992 .146 -.012
7 118 293 62 387 55 -94 109 223 70 453 46 -163 0 0 50 242 34 323 57 7 44 3 -39 -117 null null null 4.772 6.79 19.739 52 303 95.77 .06 90 2680 6870 26 35 127 136 -50 260 343 -83 null 198 -144 null null null null
8 4940 5651 56 372 4884 5278 5409 5809 61 441 5353 5436 0 0 1502 1436 24 330 100 100 100 100 10162 10789 .925 1.081 1.016 1.142 1.011 6.211 32 215 1.016 .94 70 2830 6870 27 34 143 150 0 5006 330 4675 .957 5146 4815 1.045 .9 -.063 -.153
9 101 404 55 361 45 43 96 267 59 406 40 -94 0 0 43 645 22 314 65 7 44 3 88 -54 1.047 .956 null 3.954 5.389 21.975 52 303 88.147 .12 90 2980 6870 26 35 157 166 -50 358 320 38 .846 237 -83 1.181 null -.24 null
10 99 252 54 347 45 -95 93 216 56 409 39 -131 0 0 32 231 20 310 80 3 48 1 -50 -92 null null null 4.272 14.147 37.192 52 311 41.464 .35 90 3130 6870 26 35 172 181 -50 223 307 -84 null 191 -116 null null null null
11 197 415 52 346 145 69 206 376 56 398 154 30 0 0 88 227 20 236 87 18 78 3 214 184 2.101 .476 .195 .797 .651 15.88 32 173 1.2 .09 60 3290 6870 28 34 190 196 0 368 306 61 .422 333 27 2.372 .173 -1.246 -2.535
12 248 374 65 378 182 -3 238 398 73 423 172 20 0 0 68 204 40 263 100 8 91 0 179 192 null null .116 .46 .436 15.664 12 104 -.549 -.15 50 3440 6860 27 32 205 210 0 331 335 -3 null 353 18 null .103 null -3.279
13 120 255 52 372 68 -116 125 218 56 462 73 -154 0 0 45 157 23 374 78 0 61 0 -48 -81 null null null 3.19 3.52 32.144 52 306 66.616 .2 90 3580 6870 26 35 217 226 -50 226 330 -103 null 193 -136 null null null null
14 78 274 53 361 24 -86 72 210 57 443 19 -150 0 0 32 272 29 355 40 7 17 3 -62 -131 null null null 9.9 10.315 13.957 52 291 31.777 .36 90 3730 6870 26 35 232 241 -50 243 320 -76 null 186 -133 null null null null
15 61 216 53 351 7 -135 60 197 58 443 6 -154 0 0 17 135 30 470 11 0 0 0 -128 -148 null null null 10.64 17.683 19.226 52 311 18.918 .5 90 3880 6870 26 35 247 256 -50 191 311 -120 null 175 -136 null null null null
16 305 483 53 368 252 114 304 496 57 440 250 127 0 0 57 236 24 500 100 3 100 0 366 377 2.211 .452 .508 .582 .775 11.971 32 222 1.058 .22 70 4040 6870 27 34 264 271 0 428 326 101 .401 439 113 2.495 .45 -1.319 -1.152
17 102 458 53 362 48 95 83 265 57 426 30 -97 0 0 86 865 23 289 57 13 34 9 143 -67 .505 1.979 null 5.226 3.82 20.875 52 322 64.872 .14 90 4190 6860 25 34 278 287 -50 406 321 84 1.753 235 -86 .57 null .81 null
18 59 250 53 398 5 -148 57 169 59 449 3 -229 0 0 19 257 24 289 7 5 3 3 -143 -226 null null null 24.071 19.705 12.734 52 309 52.439 .27 90 4340 6860 25 34 293 302 -50 221 353 -131 null 150 -203 null null null null
19 168 289 55 387 112 -97 178 248 60 500 122 -139 0 0 76 176 26 428 78 0 71 0 15 -17 null null null 5.325 5.866 15.664 52 338 -31.4 -.06 90 4490 6860 25 34 308 317 -50 256 343 -86 null 220 -123 null null null null
20 1325 2711 59 408 1265 2303 1440 2777 65 522 1380 2369 0 0 474 661 27 378 100 96 100 96 3568 3749 .549 1.821 1.717 1.978 1.7 7.308 32 220 1.56 .85 70 4640 6870 27 34 324 331 0 2402 361 2040 1.613 2460 2099 .62 1.521 .689 .605

Total number of rows: 44544

Table truncated, full table size 9689 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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